5T9T
Protocadherin Gamma B2 extracellular cadherin domains 1-5
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 7.5 | 295 | 8.3% (w/v) PEG8000, 16.7% (v/v) ethylene glycol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1 M Morpheus Buffer System 2 (Hepes/MOPS buffer; Molecular Dimensions) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.82 | 67.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.722 | α = 90 |
b = 118.067 | β = 103.91 |
c = 98.19 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2016-08-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.97918 | APS | 24-ID-E |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
1 | 3.5 | 40 | 99.9 | 0.369 | 0.957 | 4.8 | 3.8 | 22663 | 69.73 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.5 | 3.78 | 100 | 1.176 | 0.561 | 1.6 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5SZR | 3.5 | 39.751 | 1.34 | 22631 | 1088 | 99.92 | 0.2151 | 0.2131 | 0.2565 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.804 |
f_angle_d | 0.613 |
f_chiral_restr | 0.044 |
f_plane_restr | 0.004 |
f_bond_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7981 |
Nucleic Acid Atoms | |
Solvent Atoms | 4 |
Heterogen Atoms | 238 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |